Bi7492 DNA Sequence Analysis

Faculty of Science
Spring 2019
Extent and Intensity
2/1. 3 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. Natália Martínková, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Ladislav Dušek, Ph.D.
RECETOX – Faculty of Science
Contact Person: doc. Mgr. Natália Martínková, Ph.D.
Supplier department: RECETOX – Faculty of Science
Timetable
Mon 18. 2. to Fri 17. 5. Thu 9:00–11:50 D29/347-RCX2
Prerequisites
Students need to understand basic principles of molecular biology and genetics. Suggested courses are Neparametrické metody (K. Kubošová) and Stochastické modely (M. Budíková).
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 1/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30
Course objectives
After completing the course the student will be able:
- to formulate a hypothesis and to test it;
- to assemble a complete DNA sequence, using graphical output from sequencing;
- to use information available in genetic databases;
- to identify an unknown sequence by searching the genetic databases and comparing the hits with suitable BLAST algorithms;
- to evaluate the sequence identification;
- to calculate genetic distances, using suitable substitution model;
- to reconstruct phylogenetic trees, using distance methods, maximum parsimony, maximum likelihood and Bayesian inference;
- to interpret phylogenetic relationships in a sequence dataset and critically evaluate conflicting results.
Syllabus
  • 1. Genomics: (a) Genomes, genome organisation, variability, (b) Genome sequencing – next-gen sequencing, pyrosequencing, sequencing by ligation.
  • 2. Genome assembly: (a) De-novo, resequencing, mutation detection, (b) Contig, length and number of contigs, (c) Parameters of contig assembly, (d) Coverage – variability detection.
  • 3. Sequence search: (a) GenBank, EMBL, DDBJ, UniProt, (b) Entréz, SRS, (c) Libraries, cross-referencing.
  • 4. BLAST: (a) nucleotide and protein blast, megablast, psi-blast, (b) Search principle, (c) Result evaluation, E-value.
  • 5. Genomic sequence annotation: (a) RNA prediction, (b) Genomic islands, (c) Protein prediction – Prokaryota.
  • 6. Genomic sequence annotation: (a) Protein prediction – Eukaryota, (b) CpG islands, (c) Annotation report.
  • 7. Alignment: (a) Homologous positions, (b) Local, global alignment – assembly options, (c) Dynamic programming.
  • 8. Relationship modelling: (a) Phylogenetic tree - terminology, interpretation, (b) Tree comparison.
  • 9. Substitution model: (a) Genetic distances, (b) Model parameters, (c) Problems and solutions.
  • 10. Phylogenetics: (a) Phylogenetic analysis – neighbour-joining, maximum parsimony, (b) Significance of signal, bootstrap.
  • 11. Maximum likelihood: (a) Likelihood function, (b) Randomised accelerated maximum likelihood.
  • 12. Bayesian analysis: (a) Posterior probability, (b) Effect of priors on posterior distribution, (c) Convergence, Metropolis-coupled MCMC.
  • 13. Gene and species evolution: (a) Supermatrix, (b) Supertrees, (c) Bayesian estimation of species trees.
  • 14. Visualisation.
Literature
  • FELSENSTEIN, Joseph. Inferring phylogenies. Sunderland, Mass.: Sinauer Associates, 2004, xx, 664. ISBN 0878931775. info
  • CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Vyd. 1. Praha: Academia, 2006, 148 s. ISBN 8020013601. info
  • ZIMA, Jan. Genetické metody v zoologii. 1. vyd. Praha: Karolinum, 2004, 239 s. ISBN 8024607956. info
Teaching methods
Lectures, discussion, in-class data analysis.
Assessment methods
Five-minute tests throughout the course, final project based on student's design, verbal interpretation of the project for the final exam, final written test.
Language of instruction
Czech
Further Comments
Study Materials
Teacher's information
http://www.youtube.com/watch?v=suQSmEToTdo
The course is also listed under the following terms Autumn 2010 - only for the accreditation, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, spring 2018, Autumn 2019, Spring 2020, Autumn 2020, Spring 2021, autumn 2021.
  • Enrolment Statistics (Spring 2019, recent)
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